OxHb

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Last updated: 2023-10-14

Checks: 5 2

Knit directory: cTWAS_analysis/

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html	6a15ad1	sq-96	2023-10-14	update
Rmd	e0d796f	sq-96	2023-10-13	update

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Artery Coronary

#estimated prior inclusion probability
ctwas_parameters$group_prior

         SNP         gene 
0.0003789661 0.0048196252 

#estimated prior effect size
ctwas_parameters$group_prior_var

      SNP      gene 
0.6727008 0.5860888 

#estimated enrichment of genes over variants
ctwas_parameters$enrichment

    gene 
12.71783 

#PVE explained by genes and variants
ctwas_parameters$group_pve

       SNP       gene 
0.71103798 0.01352419 

#total heritability (sum of PVE)
ctwas_parameters$total_pve

[1] 0.7245622

#attributable heritability
ctwas_parameters$attributable_pve

       SNP       gene 
0.98133467 0.01866533 

#plot convergence
ctwas_parameters$convergence_plot

Past versions of unnamed-chunk-3-1.png

Version	Author	Date
6a15ad1	sq-96	2023-10-14

#print top genes
head(ctwas_res[ctwas_res$type=="gene",])

       chrom                 id       pos type region_tag1 region_tag2 cs_index
164440     9 ENSG00000136868.10 113209149 gene           9          58        0
263152    20 ENSG00000089177.18  16581461 gene          20          12        0
272677    22 ENSG00000184381.18  38145259 gene          22          15        0
261678    20  ENSG00000275491.1   3807832 gene          20           3        0
90495      5 ENSG00000132356.11  40798520 gene           5          27        0
117969     6 ENSG00000178425.13 116099964 gene           6          77        0
        susie_pip      mu2  genename         z
164440 0.11803156 9.216227   SLC31A1 -3.933203
263152 0.09730827 8.050336    KIF16B -3.085439
272677 0.08515657 7.548930    PLA2G6  3.053686
261678 0.08398874 7.466874 LINC01730 -2.945771
90495  0.08384722 7.723628    PRKAA1 -3.439407
117969 0.08334959 7.383582    NT5DC1  3.118395

Artery Tibial

#estimated prior inclusion probability
ctwas_parameters$group_prior

         SNP         gene 
0.0003778214 0.0040115252 

#estimated prior effect size
ctwas_parameters$group_prior_var

      SNP      gene 
0.6684344 0.5565171 

#estimated enrichment of genes over variants
ctwas_parameters$enrichment

    gene 
10.61752 

#PVE explained by genes and variants
ctwas_parameters$group_pve

       SNP       gene 
0.70439414 0.01309908 

#total heritability (sum of PVE)
ctwas_parameters$total_pve

[1] 0.7174932

#attributable heritability
ctwas_parameters$attributable_pve

       SNP       gene 
0.98174327 0.01825673 

#plot convergence
ctwas_parameters$convergence_plot

Past versions of unnamed-chunk-7-1.png

Version	Author	Date
6a15ad1	sq-96	2023-10-14

head(ctwas_res[ctwas_res$type=="gene",])

       chrom                 id       pos type region_tag1 region_tag2 cs_index
114696     6 ENSG00000005700.14  82247064 gene           6          56        0
272419    22 ENSG00000159496.14  23679302 gene          22           6        0
179945    10 ENSG00000151923.17 119601669 gene          10          74        0
151888     8  ENSG00000164841.4 108787887 gene           8          74        0
241123    16 ENSG00000040199.18  71804965 gene          16          38        0
243700    17 ENSG00000174292.12   7380407 gene          17           6        0
        susie_pip      mu2 genename         z
114696 0.11468988 9.126035     IBTK -3.787795
272419 0.08483873 7.971765     RGL4  3.286735
179945 0.08104538 7.839875    TIAL1  3.480318
151888 0.07962949 7.989882   TMEM74 -3.623924
241123 0.07790796 7.513540   PHLPP2 -3.126064
243700 0.07591772 7.535001     TNK1  3.186510

Heart Atrial Appendage

#estimated prior inclusion probability
ctwas_parameters$group_prior

         SNP         gene 
0.0003779586 0.0050855938 

#estimated prior effect size
ctwas_parameters$group_prior_var

      SNP      gene 
0.6799803 0.8693670 

#estimated enrichment of genes over variants
ctwas_parameters$enrichment

    gene 
13.45542 

#PVE explained by genes and variants
ctwas_parameters$group_pve

       SNP       gene 
0.71682145 0.02367152 

#total heritability (sum of PVE)
ctwas_parameters$total_pve

[1] 0.740493

#attributable heritability
ctwas_parameters$attributable_pve

       SNP       gene 
0.96803275 0.03196725 

#plot convergence
ctwas_parameters$convergence_plot

Past versions of unnamed-chunk-11-1.png

Version	Author	Date
6a15ad1	sq-96	2023-10-14

head(ctwas_res[ctwas_res$type=="gene",])

       chrom                 id       pos type region_tag1 region_tag2 cs_index
165901     9 ENSG00000136944.17 126565356 gene           9          65        0
57759      3 ENSG00000144908.13 126016332 gene           3          78        0
95338      5  ENSG00000250049.5  92296991 gene           5          54        0
95337      5  ENSG00000248864.1  92329276 gene           5          54        0
65473      4 ENSG00000159733.13   2395131 gene           4           3        0
224367    14 ENSG00000027075.14  61235011 gene          14          28        0
       susie_pip      mu2      genename         z
165901 0.1584757 12.62261         LMX1B  3.258848
57759  0.1535566 13.15896       ALDH1L1  3.817762
95338  0.1511946 12.76268 RP11-348J24.2  3.951225
95337  0.1505937 12.74289 RP11-348J24.1  3.943968
65473  0.1463878 12.17379       ZFYVE28  3.257767
224367 0.1338625 11.63597         PRKCH -3.100649

Heart Left Ventricle

#estimated prior inclusion probability
ctwas_parameters$group_prior

         SNP         gene 
0.0003788274 0.0054372428 

#estimated prior effect size
ctwas_parameters$group_prior_var

      SNP      gene 
0.6450365 2.3567095 

#estimated enrichment of genes over variants
ctwas_parameters$enrichment

    gene 
14.35282 

#PVE explained by genes and variants
ctwas_parameters$group_pve

      SNP      gene 
0.6815476 0.0633139 

#total heritability (sum of PVE)
ctwas_parameters$total_pve

[1] 0.7448615

#attributable heritability
ctwas_parameters$attributable_pve

       SNP       gene 
0.91499909 0.08500091 

#plot convergence
ctwas_parameters$convergence_plot

Past versions of unnamed-chunk-15-1.png

Version	Author	Date
6a15ad1	sq-96	2023-10-14

head(ctwas_res[ctwas_res$type=="gene",])

       chrom                 id       pos type region_tag1 region_tag2 cs_index
232652    15 ENSG00000137819.13  69299268 gene          15          32        0
95174      5  ENSG00000248864.1  92329276 gene           5          54        0
256443    19 ENSG00000171970.12   2897135 gene          19           3        0
176862    10 ENSG00000176273.14  93893644 gene          10          60        0
100805     5 ENSG00000070814.17 150356800 gene           5          88        0
271544    22  ENSG00000272733.1  23686225 gene          22           6        0
       susie_pip      mu2      genename         z
232652 0.3830957 28.46332         PAQR5  4.277398
95174  0.2857001 25.74061 RP11-348J24.1  3.943968
256443 0.2260197 23.52581         ZNF57 -3.403225
176862 0.2147015 23.56849       SLC35G1  3.538506
100805 0.2105803 23.08782         TCOF1  3.426022
271544 0.2065853 23.00182    KB-208E9.1  3.247406

Kidney Cortex

#estimated prior inclusion probability
ctwas_parameters$group_prior

        SNP        gene 
0.000379666 0.004579254 

#estimated prior effect size
ctwas_parameters$group_prior_var

     SNP     gene 
0.681686 2.502479 

#estimated enrichment of genes over variants
ctwas_parameters$enrichment

    gene 
12.06127 

#PVE explained by genes and variants
ctwas_parameters$group_pve

       SNP       gene 
0.72186587 0.03975231 

#total heritability (sum of PVE)
ctwas_parameters$total_pve

[1] 0.7616182

#attributable heritability
ctwas_parameters$attributable_pve

       SNP       gene 
0.94780546 0.05219454 

#plot convergence
ctwas_parameters$convergence_plot

Past versions of unnamed-chunk-19-1.png

Version	Author	Date
6a15ad1	sq-96	2023-10-14

head(ctwas_res[ctwas_res$type=="gene",])

       chrom                 id       pos type region_tag1 region_tag2 cs_index
231596    15 ENSG00000137819.13  69299268 gene          15          32        0
36106      2  ENSG00000115145.9 152176276 gene           2          91        0
221967    14 ENSG00000073712.14  52952836 gene          14          21        0
91273      5 ENSG00000177058.11  55773348 gene           5          32        0
117508     6 ENSG00000178425.13 116099964 gene           6          77        0
260478    20  ENSG00000275491.1   3807832 gene          20           3        0
       susie_pip      mu2  genename         z
231596 0.3563809 29.67982     PAQR5 -4.277398
36106  0.2477434 26.97233     STAM2  3.836622
221967 0.1606260 22.27244    FERMT2 -2.990795
91273  0.1594552 22.35682   SLC38A9 -3.307919
117508 0.1553302 22.18781    NT5DC1 -3.118395
260478 0.1502463 22.10096 LINC01730 -2.945771

Liver

#estimated prior inclusion probability
ctwas_parameters$group_prior

         SNP         gene 
0.0003814401 0.0041596106 

#estimated prior effect size
ctwas_parameters$group_prior_var

      SNP      gene 
0.7027292 1.2651829 

#estimated enrichment of genes over variants
ctwas_parameters$enrichment

    gene 
10.90502 

#PVE explained by genes and variants
ctwas_parameters$group_pve

      SNP      gene 
0.7476266 0.0231917 

#total heritability (sum of PVE)
ctwas_parameters$total_pve

[1] 0.7708182

#attributable heritability
ctwas_parameters$attributable_pve

       SNP       gene 
0.96991289 0.03008711 

#plot convergence
ctwas_parameters$convergence_plot

Past versions of unnamed-chunk-23-1.png

Version	Author	Date
6a15ad1	sq-96	2023-10-14

head(ctwas_res[ctwas_res$type=="gene",])

       chrom                 id       pos type region_tag1 region_tag2 cs_index
232268    15 ENSG00000137819.13  69299268 gene          15          32        0
95276      5  ENSG00000272021.1  95849392 gene           5          56        0
270005    21 ENSG00000160201.11  43031887 gene          21          21        0
176557    10 ENSG00000176273.14  93893644 gene          10          60        0
191545    11  ENSG00000137673.8 102530930 gene          11          59        0
103734     6 ENSG00000112699.10   2236692 gene           6           2        0
       susie_pip      mu2   genename         z
232268 0.2710718 20.70799      PAQR5 -4.277398
95276  0.1672517 17.25707 AC008592.8 -3.348117
270005 0.1395812 16.08112      U2AF1 -3.187321
176557 0.1365257 16.35490    SLC35G1 -3.538506
191545 0.1237505 17.10431       MMP7  3.217326
103734 0.1186136 15.80775       GMDS -3.273856

Lung

#estimated prior inclusion probability
ctwas_parameters$group_prior

         SNP         gene 
0.0003797659 0.0033581097 

#estimated prior effect size
ctwas_parameters$group_prior_var

      SNP      gene 
0.6790112 0.5315708 

#estimated enrichment of genes over variants
ctwas_parameters$enrichment

    gene 
8.842579 

#PVE explained by genes and variants
ctwas_parameters$group_pve

       SNP       gene 
0.71922254 0.01041293 

#total heritability (sum of PVE)
ctwas_parameters$total_pve

[1] 0.7296355

#attributable heritability
ctwas_parameters$attributable_pve

       SNP       gene 
0.98572859 0.01427141 

#plot convergence
ctwas_parameters$convergence_plot

Past versions of unnamed-chunk-27-1.png

Version	Author	Date
6a15ad1	sq-96	2023-10-14

head(ctwas_res[ctwas_res$type=="gene",])

       chrom                 id       pos type region_tag1 region_tag2 cs_index
233304    15 ENSG00000137819.13  69299268 gene          15          32        0
151315     8  ENSG00000164935.6 104341570 gene           8          71        0
271364    21 ENSG00000160201.11  43031887 gene          21          21        0
135028     7 ENSG00000160963.13 101362454 gene           7          62        0
206165    12 ENSG00000136048.13 101902056 gene          12          61        0
192366    11  ENSG00000137673.8 102530930 gene          11          59        0
        susie_pip      mu2 genename         z
233304 0.11355832 9.606008    PAQR5 -4.277398
151315 0.08171085 8.866802  DCSTAMP  3.944082
271364 0.06675872 7.344053    U2AF1 -3.187321
135028 0.06281241 7.414368  COL26A1 -3.615133
206165 0.05941452 7.182225    DRAM1  3.223839
192366 0.05497479 7.729388     MMP7  3.217326

Pancreas

#estimated prior inclusion probability
ctwas_parameters$group_prior

         SNP         gene 
0.0003791387 0.0039006092 

#estimated prior effect size
ctwas_parameters$group_prior_var

      SNP      gene 
0.6969396 0.4391335 

#estimated enrichment of genes over variants
ctwas_parameters$enrichment

    gene 
10.28808 

#PVE explained by genes and variants
ctwas_parameters$group_pve

        SNP        gene 
0.736993487 0.008557348 

#total heritability (sum of PVE)
ctwas_parameters$total_pve

[1] 0.7455508

#attributable heritability
ctwas_parameters$attributable_pve

       SNP       gene 
0.98852211 0.01147789 

#plot convergence
ctwas_parameters$convergence_plot

Past versions of unnamed-chunk-31-1.png

Version	Author	Date
6a15ad1	sq-96	2023-10-14

head(ctwas_res[ctwas_res$type=="gene",])

       chrom                 id      pos type region_tag1 region_tag2 cs_index
90503      5 ENSG00000145592.13 40793056 gene           5          27        0
261658    20 ENSG00000125818.17  1106481 gene          20           2        0
49270      3 ENSG00000114812.12 42490447 gene           3          30        0
247840    17  ENSG00000226101.1 72071669 gene          17          41        0
270029    21 ENSG00000157557.11 38806138 gene          21          18        0
222953    14 ENSG00000073712.14 52952836 gene          14          21        0
        susie_pip      mu2  genename         z
90503  0.08901000 7.071124     RPL37  3.953186
261658 0.07566466 6.306397     PSMF1 -3.324110
49270  0.07178122 6.091420     VIPR1  3.378381
247840 0.06966362 5.895581 LINC02097  3.190044
270029 0.06813460 5.936244      ETS2 -3.200392
222953 0.06115363 5.446101    FERMT2 -2.990795

Whole_Blood

#estimated prior inclusion probability
ctwas_parameters$group_prior

         SNP         gene 
0.0003797145 0.0041089502 

#estimated prior effect size
ctwas_parameters$group_prior_var

      SNP      gene 
0.6782780 0.4515726 

#estimated enrichment of genes over variants
ctwas_parameters$enrichment

    gene 
10.82116 

#PVE explained by genes and variants
ctwas_parameters$group_pve

        SNP        gene 
0.718348783 0.009142991 

#total heritability (sum of PVE)
ctwas_parameters$total_pve

[1] 0.7274918

#attributable heritability
ctwas_parameters$attributable_pve

       SNP       gene 
0.98743217 0.01256783 

#plot convergence
ctwas_parameters$convergence_plot

Past versions of unnamed-chunk-35-1.png

Version	Author	Date
6a15ad1	sq-96	2023-10-14

head(ctwas_res[ctwas_res$type=="gene",])

       chrom                 id       pos type region_tag1 region_tag2 cs_index
177030    10 ENSG00000119943.12  98387340 gene          10          62        0
95379      5  ENSG00000236882.7  95851444 gene           5          56        0
95380      5  ENSG00000272021.1  95849392 gene           5          56        0
194215    11 ENSG00000198331.10 125883330 gene          11          77        0
245150    17  ENSG00000126368.5  40092101 gene          17          23        0
100768     5 ENSG00000070814.17 150356800 gene           5          88        0
        susie_pip      mu2   genename         z
177030 0.08194366 6.590506    PYROXD2 -3.420306
95379  0.07885068 6.485879  LINC01554 -3.375656
95380  0.07679971 6.401168 AC008592.8 -3.348117
194215 0.07624593 6.758820      HYLS1  4.095459
245150 0.07585300 6.116364      NR1D1  3.146562
100768 0.07280063 6.239463      TCOF1  3.426022

Session information

sessionInfo()

R version 4.1.0 (2021-05-18)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)

Matrix products: default
BLAS/LAPACK: /software/openblas-0.3.13-el7-x86_64/lib/libopenblas_haswellp-r0.3.13.so

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] cowplot_1.1.1   ggplot2_3.4.0   ctwas_0.1.40    workflowr_1.7.0

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.9        lattice_0.20-44   getPass_0.2-2     ps_1.7.2         
 [5] assertthat_0.2.1  rprojroot_2.0.3   digest_0.6.31     foreach_1.5.2    
 [9] utf8_1.2.2        R6_2.5.1          RSQLite_2.2.19    evaluate_0.19    
[13] httr_1.4.4        highr_0.9         pillar_1.8.1      rlang_1.1.1      
[17] rstudioapi_0.14   data.table_1.14.6 blob_1.2.3        whisker_0.4.1    
[21] callr_3.7.3       jquerylib_0.1.4   Matrix_1.3-3      rmarkdown_2.19   
[25] labeling_0.4.2    stringr_1.5.0     bit_4.0.5         munsell_0.5.0    
[29] compiler_4.1.0    httpuv_1.6.7      xfun_0.35         pkgconfig_2.0.3  
[33] htmltools_0.5.4   tidyselect_1.2.0  tibble_3.1.8      logging_0.10-108 
[37] codetools_0.2-18  fansi_1.0.3       dplyr_1.0.10      withr_2.5.0      
[41] later_1.3.0       grid_4.1.0        jsonlite_1.8.4    gtable_0.3.1     
[45] lifecycle_1.0.3   DBI_1.1.3         git2r_0.30.1      magrittr_2.0.3   
[49] scales_1.2.1      cli_3.6.1         stringi_1.7.8     cachem_1.0.6     
[53] farver_2.1.0      fs_1.5.2          promises_1.2.0.1  pgenlibr_0.3.2   
[57] bslib_0.4.1       vctrs_0.6.3       generics_0.1.3    iterators_1.0.14 
[61] tools_4.1.0       bit64_4.0.5       glue_1.6.2        processx_3.8.0   
[65] fastmap_1.1.0     yaml_2.3.6        colorspace_2.0-3  memoise_2.0.1    
[69] knitr_1.41        sass_0.4.4